generateSpectrum {Cardinal}R Documentation

Generate a simulated spectrum or image

Description

Generates a simulated spectral signal, or multiple such signals, with peaks of specified intensities.

These functions are provided for backward-compatibility; new code should use simulateSpectrum and simulateImage instead.

Usage

generateSpectrum(n, peaks = 100,
    range = c(1001, 20000),
    centers = seq(
        from = range[1] + diff(range) / (peaks + 1),
        to = range[2] - diff(range) / (peaks + 1),
        length.out = peaks),
    intensities = runif(peaks, min=0.1, max=1),
    step = diff(range)/1e3,
    resolution = 500,
    noise = 0.05,
    sd = 0.1,
    baseline = 2000,
    auc = TRUE)

generateImage(data = factor(1),
    coord = expand.grid(
        x = 1:max(1, nrow(data)),
        y = 1:max(1, ncol(data))),
    peaks = length(levels(as.factor(data))),
    delta = 10,
    as = c("SImageSet", "MSImageSet"),
    ...)

Arguments

n

The number of signals to simulate.

peaks

The number of peaks in the signal.

range

A pair of numbers specifying the range of continues feature values at which the signal is measured.

centers

The values of the singal feature at which peaks occur.

intensities

The values of the intensities of the peaks, which could either be heights of the peaks or their area under the curve.

step

The step size between measurements in the feature space.

resolution

The instrument resolution. This affects the width of the peaks. Higher resolutions produce sharper peaks.

noise

A value without scale that indicates the amount of noise in the signal.

sd

Standard deviation of the intensities of the peaks.

baseline

A value without scale that indicates the shape and size of the baseline.

auc

Should the peak heights be influenced by the area under the curve? This reflects fragmentation and limited accuracy at higher mass ranges. If 'FALSE' then the peak heights correspond directly to the provided intensities.

data

Either a factor or an integer matrix. If a factor is used, the coord argument should be specified with data to indicate the arrangement of regions in the image. If a matrix is given, coord should not be specified. The image will automatically be generated with different regions corresponding to unique integers in the matrix.

coord

A data.frame with columns representing the spatial dimensions. Each row provides a spatial coordinate for the location of an element of data if data is a factor.

delta

The effect size of the difference between peaks differentiating different regions in the image (as specified by data).

as

Should the output object be an SImageSet or MSImageSet?

...

Additional arguments to pass to generateSpectrum.

Value

For generateSpectrum, a list with elements:

For generateImage(), a SImageSet or a MSImageSet.

Author(s)

Kylie A. Bemis

See Also

simulateSpectrum, simulateImage

Examples

# Generate spectra
s <- generateSpectrum(1)
plot(x ~ t, type="l", data=s)

s <- generateSpectrum(1, centers=c(2000,3000), resolution=10, baseline=3000)
plot(x ~ t, type="l", data=s)

s <- generateSpectrum(1, peaks=2, auc=FALSE, baseline=0)
plot(x ~ t, type="l", data=s)

# Generate images
data <- matrix(c(NA, NA, 1, 1, NA, NA, NA, NA, NA, NA, 1, 1, NA, NA, 
 NA, NA, NA, NA, NA, 0, 1, 1, NA, NA, NA, NA, NA, 1, 0, 0, 1, 
 1, NA, NA, NA, NA, NA, 0, 1, 1, 1, 1, NA, NA, NA, NA, 0, 1, 1, 
 1, 1, 1, NA, NA, NA, NA, 1, 1, 1, 1, 1, 1, 1, NA, NA, NA, 1, 
 1, NA, NA, NA, NA, NA, NA, 1, 1, NA, NA, NA, NA, NA), nrow=9, ncol=9)

set.seed(1)
x <- generateImage(data)

plot(x, pixel=1)
image(x, feature=1)

coord <- expand.grid(x=1:nrow(data), y=1:ncol(data))

data2 <- as.factor(data[is.finite(data)])
coord2 <- coord[is.finite(data),]

set.seed(1)
x2 <- generateImage(data=data, coord=coord, as="MSImageSet")

plot(x, pixel=1)
image(x2, feature=1)

[Package Cardinal version 2.2.6 Index]